Core 0.5.0 0.5.1 delta

From BioPerl
Jump to: navigation, search

These are detailed notes on changes made between release-0-05 and release-0-05-1.

Bio::AnnSeq
Added AnnSeq, SeqFeatureI, generics stuff
Added in EMBL parsing and stuff
Bio::AnnSeqI
Added AnnSeq, SeqFeatureI, generics stuff
Added in EMBL parsing and stuff
Bio::Annotation
Added in annotation stuff
Bio::RangeI
Added in EMBL parsing and stuff
Bio::Root::Object
Fixed uninitialized error in _display_stats() as suggested by Jason Stewart in PR#49
Bio::Search::Hit::Fasta
Initiation of the Search/ morass err project.
Processor for Fasta is now 98% functional!
Bio::Search::Hit::HitI
Initiation of the Search/ morass err project.
Try #2
Bio::Search::Processor
Initiation of the Search/ morass err project.
Processor for Fasta is now 98% functional!
Bio::Search::Result::Fasta
Initiation of the Search/ morass err project.
Processor for Fasta is now 98% functional!
Bio::Search::Result::ResultI
Initiation of the Search/ morass err project.
Try #2
Bio::SeqFeature::Generic
Added AnnSeq, SeqFeatureI, generics stuff
Stuff... ?
Fixes to SeqFeature
Bio::SeqFeatureI
Added AnnSeq, SeqFeatureI, generics stuff
Bio::SeqIO::EMBL
Removed extraneous DESTROY subs in SeqIO modules
Bio::SeqIO::Fasta
Updated SeqIO/Fasta.pm to deal with superfamily numbers (only if requested with the -superfamily tag set to something embodying truth. Added ScoringMatrix.pm and associated matrix files. Yee haw!
Simple little bug with sfnums fixed.
Superfamily fixup for Fasta.pm. New amino acid priors for ScoringMatrix.pm, as per Stephen Altschul
Regex fix.
Removed extraneous DESTROY subs in SeqIO modules
Bio::SeqIO::GCG
Removed extraneous DESTROY subs in SeqIO modules
Bio::SeqIO::Handler
Removed extraneous DESTROY subs in SeqIO modules
Bio::SeqIO::PIR
Updated SeqIO/Fasta.pm to deal with superfamily numbers (only if requested with the -superfamily tag set to something embodying truth. Added ScoringMatrix.pm and associated matrix files. Yee haw!
Removed extraneous DESTROY subs in SeqIO modules
Bio::SeqIO::Raw
Removed extraneous DESTROY subs in SeqIO modules
Bio::SeqIO::SCF
SeqIO handler to handle chromatogram SCF files.
Added binmode $fh for Win32/Mac compatability
Removed extraneous DESTROY subs in SeqIO modules
Bio::SimpleAlign
A few new methods
Bug fix concerning addition of duplicate sequences
Bio::Tools::Blast
No longer throwing an exception for hitless reports, even if a -signif criteria was used when parsing.
Fixed the -best parsing switch as reported in PR#45
Bio::UnivAln
Edits on univaln
Makefile.PL
Added generic package handler to makefile.PL
Bumping up the require to 5.004. Bumped up release version to 0.05.1. Added note in README about which modules are 5.003 incompatible.
Personal tools
Namespaces
Variants
Actions
Main Links
documentation
community
development
Toolbox